Identification of epigenetic signatures indicating cerebral palsy

ABSTRACT

In one aspect, the invention provides a method of detecting cerebral palsy in a subject. The method includes: determining a methylation state for each of a plurality of cytosine-guanine dinucleotide (CpG) sites in a sample obtained from the subject, calculating a differential methylation level based on the methylation states of the plurality of CpG sites, and comparing the differential methylation level to a predetermined reference level. When the differential methylation level deviates from the predetermined reference level, the presence of cerebral palsy is indicated in the patient.

CROSS REFERENCE TO RELATED APPLICATIONS

The application claims priority to U.S. Provisional Patent Application No. 62/603,486, filed Jun. 1, 2017, which is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

Cerebral Palsy (CP) refers to a group of movement disorders with symptoms including poor coordination, stiff or weak muscles and tremors. There is currently no biomarker-based test to confirm or rule out CP or sub-classifications of CP.

SUMMARY OF THE INVENTION

In one aspect, the invention provides a method of detecting cerebral palsy in a subject. The method includes: determining a methylation state for each of a plurality of cytosine-guanine dinucleotide (CpG) sites in a sample obtained from the subject, calculating a differential methylation level based on the methylation states of the plurality of CpG sites, and comparing the differential methylation level to a predetermined reference level. When the differential methylation level deviates from the predetermined reference level, the presence of cerebral palsy is indicated in the patient.

In various embodiments, the plurality of CpG sites comprises at least one selected from the CpG sites listed in Table 4, Table 5, Table 6 or Table 7.

In various embodiments, the plurality of CpG sites comprises at least five selected from the CpG sites listed in Table 4, Table 5, Table 6 or Table 7.

In various embodiments, the plurality of CpG sites comprises at least ten selected from the CpG sites listed in Table 4, Table 5, Table 6 or Table 7.

In various embodiments, the plurality of CpG sites comprises at least m % selected from the top n most predictive CpG sites listed in Table 4, Table 5, Table 6 or Table 7. wherein: m is selected from the group consisting of: 50, 60, 70, 80, 90, 95, and 99; and n is selected from the group consisting of: 100, 500, 1,000, 2,000, and 2,500.

In various embodiments, the method further includes providing treatment for cerebral palsy to the patient when cerebral palsy is indicated. In various embodiments, the treatment for cerebral palsy includes the administration of medication, therapy or surgery.

In various embodiments, the plurality of CpG sites includes a plurality of up sites and a plurality of down sites. Methylation at the up sites indicates that the likelihood the patient has cerebral palsy is increased. Methylation at the down sites indicates that the likelihood the patient has cerebral palsy is decreased. Calculating a differential methylation level includes adding in a linear weighted summation values based on the methylation states of the up sites from a value based on the methylation states of the down sites.

In various embodiments, the sample is selected from the group consisting of a peripheral blood mononuclear cell sample, a blood sample, a muscle sample or a satellite cell sample. The blood sample may either be a whole blood sample or a buffy coat sample.

BRIEF DESCRIPTION OF THE DRAWINGS

For a fuller understanding of the nature and desired objects of the present invention, reference is made to the following detailed description taken in conjunction with the accompanying figures.

FIG. 1 depicts sample profiles for % MET as a frequency distribution (histogram) overlaid with a probability density distribution function (filled logistic curve). The data reveal bulk profiles of methylation that were scored in the analysis described herein.

FIG. 2 is a series of graphs which depict a high-level breakdown of methylation load (ΔML) among functional class and gene structure categories to identify most active regions of methylation changes between non-CP vs CP. Differential methylation load is used as a scoring metric for considering how total methylation intensity for a given gene or gene region differs between sample groups.

FIG. 3 depicts epigenetic discrimination of methylation patterns. Using an ordinate analysis technique of non-metric multidimensional scaling (NMDS), CpG methylation profiles were compared among individuals to isolate patterns conserved within groups while also differing between groups (non-CP vs CP). The first two component axes are plotted to locate the individual sample points in a 2D plane. Ellipses drawn represent 90% confidence intervals around the position of the true group means.

FIG. 4 depicts the frequency distribution of the coefficient of variation for each CpG(i) site among sample replicates within both non-CP and CP cohorts plotted for each pairwise comparison. This reveals the level of variance among replicate measures in the analysis. A 10% reference line is shown. The inset shows the P-value significance level of the top 5,000 CpG sites scored in the pairwise analysis. Sample comparisons with low variance have highly significant differences.

FIG. 5 depicts the top 1,000 differentially methylated CpG sites in each pairwise comparison clustered with a visual heatmap of % Met scores (yellow=0% to blue=100%). These individual CpG sites are then tested for significance with a false-discovery rate correction. The resolution between non-CP and CP samples reveals quantitative separation among distinct subgroups of CpG sites.

FIG. 6 is a bar graph that depicts the P-value of groups of CpG sites by P-value cutoff.

FIG. 7 depicts a hierarchical clustering of methylation patterns among samples to identify those sites or domains with correlated shifts in methylation.

FIG. 8 is a smear plot which depicts CpG response distribution from likelihood ratio test in FIG. 7. NS=Not Significant; PVAL=P-value; FDR=False Discovery Rate.

FIG. 9 is a volcano plot that depicts CpG fold-change vs. P-value. NS=Not Significant; PVAL=P-value; FDR=False Discovery Rate.

FIG. 10 depicts differential methylation load with top 10 CpG Sites. Circular ideograms are presented with a mean subtraction of CpG methylation scores (Grp1 minus Grp2) to calculate a summation methylation load (ΔML) score across chromosomal domains. These data are presented as a scatterplot with red and green background to accentuate areas where they are most different. The correlative association between top 10 CpG sites are shown as red arcs that track the first highest correlation for each CpG site while orange arcs show the second highest. Gene labels indicate the positions of the top 60 CpG sites, with green indicating higher methylation in Grp1 and red indicating higher methylation in Grp2.

FIG. 11 contrasts overall CpG site methylation between CP and non-CP subjects. Significantly different (sigdiff) differential methylation was defined as p<0.05, was observed at 4,694 sites in muscle cells. Overall, CpG sites in CP muscle samples are more unmethylated than in Controls.

FIG. 12 depicts transcriptional start site (TSS) methylation load score in muscle cell samples. There are significantly different differential methylation load scores between CP and non-CP subjects based on CpG sites in the promoter regions of 120 annotated genes. There is no prominent overall methylation loss or gain between CP and Control in TSS domains.

FIG. 13 contrasts overall CpG site methylation between CP and non-CP subjects. SigDiff differential methylation (p<0.05, FDR) at 4,694 sites in myosatellite cells (SAT cells). Overall CpG sites in CP SAT cell samples are more slightly more unmethylated than in Controls.

FIG. 14 depicts transcriptional start site (TSS) methylation load score in SAT cell samples. There are significantly different differential methylation load scores between CP and non-CP subjects based on CpG sites in the promoter regions of 36 annotated genes. There is no prominent overall methylation loss or gain between CP and Control in TSS domains.

FIG. 15 contrasts CpG site % methylation between CPwb (Cp, whole blood samples), CNwb (non-CP, whole blood samples), CPbc (CP, buffy coat samples) and CNbc (non-CP, buffy coat samples).

FIG. 16 depicts the number of CpG sites that are significantly different between each sample type. The highlighted slice represents the 585 CpG sites that are SigDiff between CP and CN in both whole blood and buffy coat.

FIG. 17 depicts transcriptional start site (TSS) methylation load score in CPwb (Cp, whole blood samples), CNwb (non-CP, whole blood samples), CPbc (CP, buffy coat samples) and CNbc (non-CP, buffy coat samples). There are 59 unique sigdiff TSS sites in CP vs CN for whole blood. There are 109 unique sigdiff CpG sites in Cp vs CN for buffy coat. The yield of sigdiff sites is higher in buffy coat, but the discrimination between patient phenotypes is equivalent between WB and BC.

FIG. 18 depicts the number of TSS Gene sites that are significantly different between each sample type. The highlighted slice represents the 36 TSS Gene sites that are significantly different between CP and CN in both whole blood and buffy coat.

DEFINITIONS

The instant invention is most clearly understood with reference to the following definitions.

As used herein, the singular form “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise.

Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. “About” can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.

As used in the specification and claims, the terms “comprises,” “comprising,” “containing,” “having,” and the like can have the meaning ascribed to them in U.S. patent law and can mean “includes,” “including,” and the like.

As used herein, “cerebral palsy” or “CP” refers to a superfamily of disorders generally considered to be caused by damage to or abnormalities within the developing brain and associated with impaired motor function including movement, posture, and balance.

As used herein, “cytosine-guanine dinucleotide site” or “CpG site” means a cytosine nucleotide followed by a guanine nucleotide in the genome of an organism. CpG sites can be designated with the number of the chromosome of the organism on which they are located and a number designating the position. The flanking sequences can be used to generate the position number. For example, “12.108079458” or “chr12 108079458” refer to a CpG site on chromosome 12 at position 108079458. The position number refers to the nucleotide index starting from 1 on the coding or plus (+) strand of the DNA molecule and specifically references the position of the 5′ cytosine in a CpG dinucleotide pair. In addition, this CpG location has a complementary sequence pair on the non-coding minus (−) strand and the position number also refers to that complementary strand cytosine which is located plus one nucleotide from the indicated coding strand position. Thus, for CpG 12.108079458, the methylation score values indexed to this specific site cover the cytosine on the coding strand of chromosome 12 at position number 108079458 and the cytosine on the non-coding strand of chromosome 12 at position number 108079459.

As used herein, “methylation” or “methylated” as applied to CpG sites refers to the addition of a methyl group to cytosine, forming either 5′-methyl-cytosine or 5′-hydroxymethyl-cystosine.

As used herein, the term “percent methylation” or “% MET” refers to the frequency with which a particular set of CpG sites are methylated. Here, CpG methylation is expressed as a percentage of methylated copies found in the DNA sample for each individual CpG site relative to the total number of copies found for each site.

A “reference level” with respect to some measurement used in diagnosis is indicative of the presence or absence of a particular phenotype or characteristic. When the level of the measurement in a subject deviates from the reference level it is indicative of the presence of, or relatively heightened level of, a particular phenotype or characteristic.

Unless specifically stated or obvious from context, the term “or,” as used herein, is understood to be inclusive.

Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 (as well as fractions thereof unless the context clearly dictates otherwise).

DETAILED DESCRIPTION OF THE INVENTION

Conclusive diagnosis of CP is valuable because it is a prerequisite for intervention and affords peace of mind to the patient and family. Accordingly, there is a need for an efficient and accurate test for CP. This disclosure addresses that need.

One aspect of the invention provides a method of detecting cerebral palsy in a subject. The method can include: determining a methylation state for each of a plurality of CpG sites in a sample obtained from the subject, calculating a differential methylation level based on the methylation states of the plurality of CpG sites, and comparing the differential methylation level to a predetermined reference level. Deviation of the methylation load level from the predetermined reference level indicates the presence of cerebral palsy in the patient.

The methylation state of the plurality of CpG sites may be determined by any means known in the art. In various embodiments, the methylation state of the plurality of CpG sites may be determined by methyl-sensitive restriction enzyme digestion followed by Next-Gen Sequencing on an appropriate instrument, or they may be determined by targeted qPCR assays to quantify cut and uncut CpG sites following methyl-sensitive restriction enzyme digestion, or they may be determined by bisulfite oxidation treatment with DNA sequencing (either direct or via NGS), or they may be determined by hybridization of labelled oligonucleotide probes (called “hybridization arrays”) to measure methylation following methyl-sensitive restriction enzyme digestion, or they may be determined by hybridization of anti-5′-methyl-cytosine antibodies to measure methylation after hybridization capture on a targeted gene panel.

Without wishing to be limited by theory, in various embodiments, the method relies on the concept of differential methylation level (ΔML)—site-specific differences in CpG methylation summed across a gene or genome domain, structure or element—in order to characterize functional shifts in methylation patterns. This method is illustrated in the example below and in Equation (1).

As shown in FIGS. 5 and 6, the methylation state of the majority of CpG sites in the genome are not significant predictors of CP in a patient. However, determining the methylation state of a certain subset of CpG sites and applying the algorithm outlined above or a derivative classification algorithm one may be used to detect CP. The plurality of CpG sites in the present aspect of the invention refers to sites selected from this predictive subset of sites. In various embodiments, the sites may be selected from Table 4, Table 5, Table 6 and Table 7.

In various embodiments, the plurality of CpG sites includes a plurality of “up sites” and a plurality of “down sites”. Up sites are CpG sites where methylation at the site indicates an increased methylation load in CP patients relative to non-CP matched control patients. Down sites are CpG sites where methylation at the site indicates a decreased methylation load in CP patients relative to non-CP matched control patients. Table 3 illustrates one possible approach by which these sites may be scored in order to determine ΔML.

Various embodiments of the invention are directed to methods of examining sets of up sites and down sites and determining a differential methylation level based on their methylation state. Due to the predictive value of the plurality of sites, the scores will differ when examining patients with and without CP.

A predetermined reference level may be calculated by determining the methylation state of a set of sites in patients who are known not to have CP. Accordingly, when a differential methylation level is determined using the same plurality of site, deviation from the reference level indicates an additional evidentiary datum point supporting increasing the probability that the patient likely has CP.

A skilled person will understand that the specifics of the calculation used for generating a differential methylation level are not critical and various processes may be employed to generate these levels. All of them are within the scope of various embodiments of the invention.

Various embodiments of the invention rely on pluralities of CpG sites of various sizes. In various embodiments, the plurality of CpG sites may contain about 5, 10, 100, 1000, 5000 or more CpG sites.

Even among the CpG sites that have shown predictive power, different sites contribute different weightings to the overall predictive probability of the CP status of a patient. Various embodiments of the invention calculate differential methylation levels based on various combinations of predictive CpG sites.

The predictive power of the sites may be quantified in various ways. As shown in FIG. 3, the deviation between the reference level (non-CP) and the differential methylation level for patients with CP can be represented by non-metric multidimensional scaling (NMDS). Each site in the set will make a contribution to the ordinate discrimination in the NMDS. In some embodiments, the plurality of CpG sites includes one or more sites selected from Table 4, ranked by the site's contribution to ordinate discrimination. Table 6 lists the top 1000 CpG sites for blood, muscle and muscle satellite cell samples by P-value.

The predictive power of CpG sites may also be quantified based on P-value, adjusted for False Discovery Rate (FDR). Table 5 lists the top 40 CpG sites for peripheral blood mononuclear cell samples by P-value. In various embodiments, the plurality of CpG sites may include one or more sites selected from Table 5. In some embodiment, the plurality of CpG sites may include the top n sites or m of the top n sites from Table 5 or other ordinal lists (wherein m and n are positive integers). Table 7 lists the top 1000 CpG sites for blood, muscle and muscle satellite cell samples by P-value.

In various embodiments, the method further includes providing treatment for CP to patients in whom CP is indicated. The treatment may include any form of standard of care treatment for CP accepted by the extended medical community. CP as a group of disorders includes many variations that require various interventions to improve the quality of life of the CP patient and any of these may be included in various embodiments of the invention.

The method may be practiced by analyzing a variety of sample types. In various embodiments, the sample may be a peripheral blood mononuclear cell sample, a blood sample, a muscle cell sample or muscle satellite cell sample. In various embodiments, the sites selected from Table 4, Table 5, Table 6 or Table 7 can be matched to the sample type used.

In various embodiments the treatment for CP may include surgery. In various embodiments, the surgery may include gastroenterology surgery, hearing correction surgery, medicine related surgery, e.g. insertion of a baclofen pump, orthopedic surgery, neurosurgery, urologic surgery and vision correction surgery.

In various embodiments the treatment for CP may be therapy. In various embodiments the therapy may include occupational therapy, physical therapy and speech therapy.

In various embodiments, the treatment for CP may include the administration of medication. In various embodiments the administration of medication may include medication to treat seizures, involuntary movement, spasticity, incontinence and gastroesophageal reflux. In various embodiments the treatment for CP may include anticonvulsants, muscle relaxants, benzodiazepines, nerve blocks, botulinum toxin (BTX) (available, e.g., under the BOTOX® trademark from Allergan, Inc. of Irvine, Calif.), baclofen and anticholinergics.

Experimental Example

The invention is further described in detail by reference to the following experimental example. This example is provided for purposes of illustration only, and is not intended to be limiting unless otherwise specified. Thus, the invention should in no way be construed as being limited to the following example, but rather, should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.

Example 1

A cohort of 34 patients was identified and genomic DNA was extracted from each patient. Samples were prepared for sequencing analysis using a methyl-sensitive restriction enzyme digestion and library preparation followed by Next-Gen Sequencing (NGS) on an ILLUMINA® HISEQ® X10™ system with >30× coverage. Sequencing data was uploaded to secure cloud-based computational infrastructure where it was processed and analyzed for site-specific DNA methylation profiles.

The samples used in this study are listed in Table 1 with the codes employed for analyses and the genomic DNA QC values. The sequencing vendor Macrogen, Inc. performed a second round of QC upon sample receipt. Genomic DNA samples received from Nemours Biomedical Research Center were coded internally with GP numbers. DNA quantity and quality used for sequencing is reported in the data columns.

TABLE 1 Sample Identification Codes. Blinding Code ng/uL A260 260/230 260/280 Total ug 10 518.57 10.371 2.35 1.88 10.3714 28 2867.9 57.36 2.32 1.87 57.358 370 982.95 19.659 2.3 1.91 19.659 375 1327.1 26.542 2.34 1.92 26.542 376 263.82 5.276 2.35 1.91 5.2764 380 1049.7 20.995 2.08 1.76 20.994 414 264.88 5.298 2.18 1.91 5.2976 416 1447.9 28.959 2.31 1.91 28.958 417 510.25 10.205 2.29 1.88 10.205 425 664.05 13.281 2.28 1.85 13.281 431 1216.6 24.334 2.33 1.92 24.332 436 1596.8 31.937 2.31 1.91 31.936 440 4258 85.7 2.09 1.7 85.16 444 418.42 8.368 2.38 1.89 8.3684 466 517.38 10.348 1.65 1.58 10.3476 489 543.51 10.87 2.3 1.88 10.8702 515 1724.4 34.49 2.34 1.91 34.488 527 1611.8 32.236 2.32 1.9 32.236 563 2060.7 41.216 2.32 1.9 41.214 573 1405 28.102 2.16 1.91 28.1 583 2301.6 46.033 2.28 1.89 46.032 584 1794.9 35.9 2.33 1.9 35.898 597 383.91 7.678 2.22 1.91 7.6782 605 3157.9 63.158 2.32 1.86 63.158 533 3132.20 62.644 2.25 1.86 62.6 568 2294.30 45.887 2.32 1.89 45.9 600 2377.20 47.545 2.37 1.85 47.5 606 135.75 2.715 3.01 1.93 2.7 45 1340.3 26.807 2.44 1.92 26.8 50 338.85 6.777 2.43 1.90 6.8 39 889.07 17.781 2.37 1.88 17.8 53 1367.70 27.355 2.41 1.88 27.4 56 3760.60 75.213 2.22 1.82 75.2 57 2528.10 50.563 2.30 1.88 50.6

Statistical analyses were conducted for pairwise contrasts using a code system of “xGrp1.xGrp2” where Grp1 and Grp2 designate the sample groups as: non-CP (CN) and Cerebral Palsy (CP). When differential methylation loads (ΔML) are presented, those values are calculated as the difference of Grp1 minus Grp2. Thus, if ΔML>0, methylation in Grp1 is greater than in Grp2 and vice versa. The specific contrasts with sample information are presented in Table 2 (below).

TABLE 2 Samples Code Grp1 Grp2 Group 1 - Group 2 Pairwise Non-CP CP KR039, KR053, KR056, KR057, - KR010, KR028, KR045, KR050, Contrasts KR370, KR380, KR414, KR416, KR375, KR376, KR417, KR440, CNvCP KR425, KR431, KR436, KR466, KR444, KR533, KR568, KR573, KR489, KR527, KR563, KR584 KR583, KR597, KR600, KR606

Note that the statistical results reported in this document utilized a total patient cohort size of 32 (16 CN vs 16 CP) after two samples were omitted due to young age of patients (<5 yo).

ΔML was calculated as the summation of the difference in % MET scores for each CpG site within the defined region or structure being scored, averaged by the number of CpG sites present:

$\begin{matrix} {{\Delta \; {ML}} = {\sum\limits_{i = {first}}^{last}\left\lbrack {{CpG}_{{\lbrack i\rbrack}{\lbrack{{Grp}\; 1}\rbrack}} - {CpG}_{{\lbrack i\rbrack}{\lbrack{{Grp}\; 2}\rbrack}}} \right\rbrack}} & (1) \end{matrix}$

where first and last CpG indexes are defined by the gene unit across which the summation score is being calculated. As the calculation is applied in Example 1, Grp1 is a control (non-CP) cohort and Grp2 contains patients with CP. Thus, positive ΔML values indicate more methylation present in Grp1 and negative values indicate more methylation in Grp2.

In this study, results from 5 levels of analyses were compared: (a) single CpG sites, (b) CpG Islands, (c) micro-CpG Islands, (d) 2 kb upstream promoter domains, and (e) Transcriptional Start Site (TSS) domains. The single CpG sites are simply the comparison of the individual site methylation score values. The CpG Islands are defined by the UCSC Genome Browser bed file and contain domains with greater than 50% G+C nucleotide content, greater than 0.60 ratio of Observed to Expected frequency of CpG sites, and a minimum length of 200 nucleotides. A subset of smaller domain definitions was also employed. The TSS domains are demarcated as a 2 kb window centered on the TSS (+/−1 kb down/up-stream). The methylation signal across the larger domain structures were all non-informative. This means that a discriminating signal was only observed at the level of single CpG site scores. Only the CpG data is included here in this report.

The pairwise analysis in Table 2 provides a direct contrast and allows for several graphical visualization plots to be generated these are presented in FIGS. 1-9. Statistically, the most robust analytical results are obtained from the multiway analysis, presented in FIG. 5. A Likelihood-Ratio-Test with one-way ANOVA-defined contrasts was used to establish a more conservative assessment than the pairwise comparisons because there is a better estimate of the false discovery rate (FDR) when the measurement variances for all samples are included as one total set. In all cases where P-values are reported in this document, significance is determined from this group multiway analysis after FDR correction.

Table 3 presents summation counts of the significant changes in methylation scores based on P-values adjusted for site-specific false discovery rates (FDR). The comparisons are executed as non-CP-minus-CP cohorts in the treatment code header, such that positive values mean methylation in the non-CP cohort is greater (UP) and negative values mean methylation in the CP cohort is greater (DOWN). Site-specific dispersion was estimated to equalize CpG variances. A Likelihood Ratio Test was used with a defined one-way ANOVA model for pairwise tests.

TABLE 3 Significant UpDown Changes in Methylation Scores. CNvCP: CpG Sites Change 0 xCP · xCN Down: −1 NA 2811 Ns: 0 NA 1524163 UP: +1 NA 3781 ns = “not significant”; Response = UP or DOWN in non-CP relative to CP cohort.

The following tables rank CpG sites according to various metrics associated with their predictive power or their location in various genes or pathways.

TABLE 4 Top 40 CpG Sites. Rank ordered listing of CpG sites contributing the most to the ordinate discrimination in the NMDS analysis. CHR POS DOMAIN UniProt GO.terms chr12 108079458 upstr B4DJV5 transcription; protein.binding; chr12 6446797 intron F5H6Z2 positive.regulation.; modulation.by.virus.; prostaglandin.me chr12 6445005 intron F5H6Z2 positive.regulation.; modulation.by.virus.; prostaglandin.me chr13 33220266 intron A9IYQ1 binding; mitotic.sister.chrom; regulation.of.cell.p; mitotic chr12 1704443 intron F5GYM2 receptor.binding; negative, regulation.; Wnt.signaling.pathwa chr6 169653176 intron Q5R153 cell.adhesion; negative.regulation.; heparin.binding; calciu chr18 4068725 intron A0A0A0MTP4 cell-cell.signaling; synaptic.transmissio; protein.binding chr12 58160354 upstr V9GYP0 positive.regulation.; positive.regulation.; calcitriol .biosy chr22 33197965 na A0A0A0MR68 neurotransmitter.sec; catalytic.activity; ATP.binding; prote chr11 71160096 intron E9PRL8 7-dehydrocholesterol; regulation.of.choles; sterol.biosynthe chr3 197687858 intron F8WcE5 cell.adhesion; mitosis; metal.ion.binding; proteolysis; meta chr18 3771925 intron A0A0A0MTP4 cell-cell.signaling; synaptic.transmissio; protein.binding chr6 150284688 upstr Q9BZM6 natural.killer.cell.; natural.killer.cell.; natural.killer.c chr3 147130343 exon Q15915 metal.ion.binding; regulation.of.smooth; positive.regulation chr18 29214163 intron J3QQY9 keratan.sulfate.meta; keratan.sulfate.bios; protein.N-Iinked ch19 20188618 upstr Q03938 regulation.of.transc; nucleic.acid.binding; DNA.binding; met chr13 28497262 intron P52945 response.to.vitamin; type.B.pancreatic.ce; detection.of.gluc chr7 130353922 exon c9JVS7 unk chr6 7394523 intron E9PFQ8 transferase.activity; protein.phosphorylat; protein.kinase.a chr19 40723542 exon Q8N6N2 protein.binding; biological.process; molecular.function chr15 99344316 intron HOYLE7 inactivation.of.MAPK; insulin-Iike.growth.; insulin.binding; chr11 32112972 exon HOYDA4 in.utero.embryonic.d; camera-type.eye.deve; calcium.ion.bind chr11 188098 intron E9PQJ6 protein.binding; SNAP.receptor.activi; retrograde.transport; chr12 121082579 intron C9J8G2 nuclear.localization; enzyme.inhibitor.act; negative.regulat chr17 11145564 intron V9GZ25 unk chr20 5081567 exon Q5JWB9 unk chr3 182928999 intron Q9J326 regulation.of.Rho.pr; Rho.guanyl-nucleotid; protein.binding chr12 5019351 5utr Q09470 potassium.ion.transm; delayed.rectifier.po; potassium.channe chr13 93896533 intron Q9Y625 phototransduction; chondroitin.sulfate.; retinoid.metabolic. chr11 32113404 intron H0YDA4 in.utero.embryonic.d; camera-type.eye.deve; calcium.ion.bind chr17 7975795 upstr 075342 Iinoleate.9S-Iipoxyg; establishment.of.ski; arachidonate.12- chr16 58000211 intron H3BQc3 intracellular.cAMP.a; intracellular.cGMP.a; Iigand-gated.ion chr18 57357804 intron A0A0A0MS88 lymphangiogenesis; venous.blood.vessel.; collagen.binding; c chr11 6633681 upstr Q12962 histone.deubiquitina; histone.H3.acetylati; histone.acetyltr chr6 26235050 exon P16402 nucleosome.assembly; DNA.binding; protein.binding; nucleosom chr12 69005196 intron F5H7Y6 regulation.of.cell.j; Rap.protein.signal.t; energy.reserve.m chr16 50582980 intron Q969G9 negative.regulation.; positive.regulation.; regulation.of.ce chr12 4758511 intron H0YGX0 transferase.activity; protein.phosphorylat; protein.kinase.a chr11 94276724 upstr F5H116 piRNA.binding; DNA.methylation.invo; piRNA.metabolic.proc; m chr18 44542946 exon K7EPQ6 ATP.binding; protein.binding; four-way.junction.he; nucleosi

The predictive power of each CpG site may be ranked by the P-value of the individual sites in differentiating between non-CP and CP patients. Table 5 ranks the top 40 sites by P-value.

TABLE 5 CpG Site logFC FDR adj P-val Response Gene Description chr3.0170984628 1.72 5.54e-33 up ENSG00000154310 NP.001155035 chr12.0113912958 −1.49 1.26e-25 down ENSG00000257935 NP.071758 chr5.0021333675 5.11 3.26e-24 up ENSG00000249359 — chr1.0000565262 −3.69 2.81e-23 down ENSG00000230021 XP.003403763 chr18.0059002180 1.22 7.40e-20 up ENSG00000101542 NP.114097 chr22.0021469408 2.02 8.36e-19 up ENSG00000169668 — chr16.0002689275 −1.31 8.83e-18 down ENSG00000205918 — chr12.0006446797 1.83 9.62e-18 up F5H6Z2 — chr15.0028343785 −1.24 8.96e-17 down ENSG00000104044 — chr6.0161033995 1.10 1.60e-16 up ENSG00000198670 NP.005568 chr18.0004068725 1.30 1.60e-16 up A0A0A0MTP4 — chr12.0001704443 −1.23 1.89e-16 down F5GYM2 — chr11.0013984067 1.25 4.52e-16 up ENSG00000152268 — chr2.0243078103 1.49 1.40e-15 up ENSG00000220804 NP.776182 chr19.0020188618 1.14 1.68e-15 up ZNF90 zinc finger protein 90 chr6.0169653176 −1.14 1.81e-15 down Q5RI53 — chr6.0007394523 1.11 1.82e-15 up E9PFQ8 — chr6.0117587149 1.15 5.81e-15 up ENSG00000170162 NP.872586 chr12.0058160354 1.26 5.81e-15 up V9GYP0 — chr13.0033220266 −1.18 1.67e-14 down A9IYQ1 — chr12.0002113367 −1.07 2.95e-14 down ENSG00000151065 — chr13.0114547107 −1.06 2.99e-14 down ENSG00000183087 NP.001137418 chr18.0029214163 1.16 7.46e-14 up J3QQY9 — chr11.0071160096 −1.10 2.45e-13 down E9PRL8 — chr3.0182928999 1.07 4.68e-13 up C9J326 — chr6.0150284688 1.20 6.75e-13 up ULBP1 UL16 binding protein 1 chr11.0093475384 1.07 1.35e-12 up ENSG00000166012 — chr16.0030886974 −1.15 1.35e-12 down ENSG00000099385 NP.004756 chr17.0007975795 1.18 1.79e-12 up ALOX12B arachidonate 12-lipoxygenase chr6.0167001337 1.09 1.85e-12 up ENSG00000071242 — chr22.0038022735 0.974 2.08e-12 up ENSG00000100083 NP.001001561 chr12.0108079458 −1.26 2.33e-12 down B4DJV5 — chr11.0000188098 −0.94 2.70e-12 down E9PQJ6 — chr3.0147130343 −1.04 3.41e-12 down ZIC1 Zic family member 1 chr13.0050656618 −1.40 4.13e-12 down ENSG00000231607 — chr3.0197687858 −1.01 4.36e-12 down F8WCE5 — chr6.0149354426 0.950 4.88e-12 up US uronyl 2-sulfotransferase chr6.0026235050 1.06 5.30e-12 up HIST1H1D T histone cluster 1 H1 family me chr17.0011145564 −0.92 5.45e-12 down V9GZ25 — chr9.0033025770 −0.92 8.48e-12 down ENSG00000086061 —

TABLE 6 Top 1000 CpG Sites. Rank ordered listing of CpG sites contributing the most to the ordinate discrimination in the NMDS analysis. Blood Muscle Satellite CHR POS CHR POS CHR POS chr12 108079458 chr16 2184051 chr18 12884805 chr12 6446797 chr15 72956969 chr13 57713776 chr12 6445005 chr12 62584454 chr13 93896533 chr13 33220266 chr14 74179572 chr20 60998493 chr12 1704443 chr12 5019004 chr20 5829089 chr6 169653176 chr20 60998493 chr16 2176197 chr18 4068725 chr16 67969342 chr17 18941025 chr12 58160354 chr6 134495313 chr20 48755321 chr22 33197965 chr14 35590507 chr12 8234476 chr11 71160096 chr17 32964775 chr11 67044849 chr3 197687858 chr16 14818378 chr14 96728320 chr18 3771925 chr17 18941025 chr14 24615469 chr6 150284688 chr13 114105414 chr13 114107632 chr3 147130343 chr12 8234476 chr20 60852455 chr18 29214163 chr14 24615469 chr12 105114308 chr19 20188618 chr13 28195784 chr15 92982723 chr13 28497262 chr20 61049813 chr12 57608666 chr7 130353922 chr6 150284688 chr14 24878082 chr6 7394523 chr12 129079508 chr15 69516868 chr19 40723542 chr22 42915052 chr12 662536 chr15 99344316 chr16 12020100 chr20 61976483 chr11 32112972 chr20 43513649 chr12 83436417 chr11 188098 chr3 111280409 chr17 19045779 chr12 121082579 chr12 105008942 chr17 53343752 chr17 11145564 chr14 103987474 chr18 11747918 chr20 5081567 chr22 37897522 chr12 25101805 chr3 182928999 chr12 105114308 chr19 48673525 chr12 5019351 chr17 65040349 chr20 36915727 chr13 93896533 chr17 19045779 chr22 42915052 chr11 32113404 chr13 28196417 chr12 67663301 chr17 7975795 chr20 37356960 chr3 111280409 chr16 58000211 chr18 499464 chr16 21610035 chr18 57357804 chr17 73029804 chr13 28550394 chr11 6633681 chr3 197676776 chr13 33765016 chr6 26235050 chr3 59803935 chrX 49178276 chr12 69005196 chr16 19728830 chr14 104190006 chr16 50582980 chr3 119422009 chr14 50108699 chr12 4758511 chr6 139013304 chr12 129065948 chr11 94276724 chr14 99984633 chr12 62584454 chr18 44542946 chr11 22647259 chr14 104497547 chr20 48552544 chr14 88459020 chr12 6334026 chr2 200819443 chr12 125026886 chr17 73510671 chr18 77267918 chr20 13971342 chr12 123753032 chr13 21141519 chr11 70664922 chr12 32908207 chr16 48639869 chr15 40886106 chr11 123045794 chr16 23706114 chr17 7975795 chr12 49484577 chr12 5019004 chr17 26166996 chr17 19046425 chr13 96206439 chr6 39029929 chr14 100005173 chr20 43513649 chr15 93351469 chr13 99650742 chr11 71951989 chr12 9103333 chr5 169695009 chr3 32022182 chr9 131710795 chr20 31128317 chr11 93063959 chr12 58088346 chr3 49044952 chr5 115178530 chr14 24900076 chr13 96137813 chr20 633169 chr20 55974298 chr3 122711856 chr6 149354426 chr6 139349539 chr14 24900076 chr6 26596052 chr12 6931525 chr18 12254395 chr19 920756 chr13 108103040 chr12 1742005 chr14 45431943 chr11 796607 chr20 31129482 chr22 30821443 chr5 65124116 chr18 77209053 chr15 60302054 chr12 8662310 chr15 27574055 chr3 42740649 chr13 57713776 chr11 8255902 chr6 145853785 chr12 49484577 chr11 2408146 chr8 68877277 chr18 12885184 chr6 1313218 chr3 12883119 chr17 73042810 chr3 48647168 chr11 66312805 chr14 58638067 chr14 104119867 chr12 54409525 chr12 49208971 chr12 103344694 chr3 159563262 chr10 23479600 chr19 33896553 chr14 24584488 chr16 2184447 chr16 62003103 chr15 22052629 chr22 24816977 chr16 87893023 chr12 5992325 chr17 11145564 chr15 45927689 chr16 4817451 chr19 15580788 chr20 52825772 chr16 2176197 chr12 95038500 chr15 60297395 chr11 67204130 chr16 1822579 chr14 38071393 chr11 65688012 chr16 88716590 chr13 107176083 chr15 62359382 chr12 119596461 chr14 50108792 chr17 48172954 chr12 50236157 chr15 21059321 chr15 77713456 chr20 60985334 chr20 41534983 chr14 80170888 chr5 142150994 chr20 61000773 chr16 53538293 chr12 58232795 chr15 90964193 chr12 6310543 chr11 122933736 chr19 14089299 chr15 21071194 chr11 63932756 chr15 41794568 chr18 74204568 chr15 27604283 chr12 96253081 chr17 4850081 chr17 73042472 chr15 57680681 chr16 14818378 chr13 20711116 chr18 44547036 chr3 110791724 chr3 132136984 chr12 121647855 chr16 70557879 chr5 134094725 chr16 31193471 chr6 39174327 chr5 50681152 chr6 26157100 chr16 70834848 chr18 25757350 chr14 93019588 chr2 112826693 chr14 74770110 chr15 72946822 chr18 11986236 chr20 31330621 chr18 44542946 chr3 147128690 chr6 143859047 chr20 61867349 chr12 116710705 chr16 66864962 chr17 11390406 chr8 97166862 chr14 100626499 chr13 96130928 chr22 37977772 chr16 9185813 chr11 63932756 chr12 5992812 chr11 61249527 chr17 31110221 chr5 149524459 chr12 16064519 chr17 38475164 chr18 10938440 chr22 43627738 chr12 65671739 chr11 124823462 chr12 96428593 chr5 13939870 chr3 197676776 chr20 61428843 chr18 44551594 chr13 96206771 chr20 25834932 chr16 2478353 chr11 1776846 chr14 58618103 chr12 57985699 chr6 169651645 chr2 3381822 chr14 100040905 chr14 103575195 chr11 13690984 chr14 91842116 chr18 43419102 chr6 56716681 chr15 75164896 chr9 21967489 chr12 106696764 chr18 56391319 chr18 13895717 chr15 39873517 chr14 23070923 chr14 64687513 chr14 45605573 chr12 113902624 chr17 40610021 chr12 48214000 chr11 2800586 chr14 24906444 chr17 15902161 chr16 70734806 chr6 10695540 chr20 32011265 chr11 35641938 chr17 80272432 chr20 25254024 chr16 2004921 chr22 39417803 chr12 12764809 chr14 76178021 chr12 96429846 chr20 60852455 chr20 62173702 chr11 67034843 chr13 28497262 chr12 124964851 chr2 153450964 chr6 73879011 chr5 124079989 chr14 93125680 chr12 118540534 chr16 48419832 chr5 170869818 chr18 44556541 chr13 52194967 chr2 38978853 chr5 168726909 chr22 31890427 chr18 10483180 chr17 19046425 chr12 12016676 chr20 44639931 chr5 79378854 chr22 20244288 chr20 20434395 chr22 39410193 chr11 7563239 chr19 56616939 chr16 4290800 chr12 58021713 chr14 42075406 chr6 167765060 chr12 123753445 chr11 20784643 chr2 129063272 chr20 48727980 chr18 20514217 chr6 3742885 chr11 821322 chr11 65744445 chr10 26501357 chr12 20568666 chr16 83967135 chr12 43944977 chr13 21286449 chr20 31058476 chr15 78287064 chr14 34406142 chr20 61584448 chr5 129242435 chr12 18457486 chr3 50230579 chr12 53044536 chr16 19728830 chr11 68672559 chr16 50746190 chr12 6450539 chr3 184278878 chr15 75967934 chr18 61160438 chr15 62360962 chr14 34720964 chr14 96002525 chr12 103980970 chr15 38545505 chr3 16419520 chr17 79800852 chr2 73299016 chr3 13920075 chr12 19398518 chr12 96429846 chr20 18447458 chr17 53343752 chr20 55800172 chr12 129072067 chr12 118540949 chr17 26989567 chr13 40149904 chr22 31886188 chr11 126367330 chr12 124196312 chr9 125674963 chr20 40822059 chr11 2405177 chr15 80452978 chr6 78172408 chr13 95256511 chr3 39449150 chr3 189791239 chr13 47191668 chr3 42646477 chr19 18366297 chr3 189791239 chr13 47250475 chr12 57639448 chr2 10200647 chr3 42262164 chr20 633169 chr20 61428843 chr11 10229941 chr2 27273727 chr18 46475320 chr16 30104676 chr20 24450876 chr16 77912976 chr18 50319582 chr5 176766295 chr20 8790229 chr13 111837470 chr5 172572092 chr6 75912320 chr11 65486827 chr12 7342661 chr12 57602992 chr17 4440254 chr5 106822941 chr5 106822941 chr12 8662310 chr3 196750460 chr3 196595774 chr11 100045994 chr8 145017702 chr3 147130343 chr12 114348940 chr5 142054203 chr17 28803808 chr12 119419907 chr6 169653572 chr14 72980894 chr3 184081196 chr2 73518897 chr12 58145283 chr2 63279693 chr6 158019037 chr5 11535023 chr19 48673525 chr20 32407915 chr11 70369651 chr12 5985138 chr13 32984305 chr17 73042810 chr11 75139544 chr12 124964851 chr9 34380008 chr20 43513977 chr18 43419097 chr12 12764809 chr12 104218860 chr14 24878082 chr11 123016467 chr14 103396312 chr16 4975267 chr16 89778878 chr6 73676215 chr11 57334814 chr13 26538260 chr16 89785669 chr16 62003103 chr12 54424611 chr13 99737576 chr14 103575195 chr2 73518897 chr7 21466431 chr14 74708903 chr22 32954811 chr17 79881668 chr13 110951025 chr5 177199729 chr18 7116462 chr22 50747228 chr16 680326 chr16 23653028 chr9 113798881 chr16 775102 chr3 48514843 chr19 46366124 chr12 112226092 chr2 74777409 chr12 57602992 chr12 123319333 chr18 14129770 chr2 203777474 chr9 79793512 chr18 21768319 chr12 121648196 chr9 37001589 chr9 134056175 chr6 10163569 chr20 7905990 chr8 11415889 chr16 84404119 chr17 64333731 chr3 39425054 chr17 61778909 chr14 52478367 chr19 39832370 chr12 58145283 chr20 31150534 chr11 74304021 chr11 123431994 chr12 128790228 chr13 32663317 chr12 49727102 chr12 31881631 chr15 45927689 chr11 64511391 chr18 57193836 chr11 102448364 chr12 96253081 chr20 5748204 chr3 45837192 chr6 157855779 chr11 70384416 chr11 118230644 chr20 30030504 chr13 33220266 chr11 48109991 chr15 40014219 chr12 96116260 chr16 21610035 chr17 28705169 chr12 120884574 chr3 112013079 chr20 2739975 chr18 4068725 chrX 48648229 chr15 53833309 chr3 20088712 chr11 63246601 chr16 4987613 chr19 7038916 chr3 13894328 chr15 39873937 chr12 109870635 chr11 130320107 chr17 31110221 chr16 583839 chr12 53460222 chr20 62150177 chr20 40172803 chr16 77953169 chr13 96137813 chr20 55970900 chr14 71108090 chr6 108436542 chr2 218771815 chr22 42914550 chr16 77912976 chr3 124501859 chr13 94830546 chr15 75943842 chr14 51134117 chr6 117997665 chr11 57308986 chr16 84042148 chr11 65308645 chr16 810757 chr20 3139415 chr11 74303282 chr14 104073702 chr6 16145414 chr8 22457903 chr19 46993480 chr11 62494490 chr19 50919627 chr14 96857563 chr15 89182360 chr6 35420737 chr17 77764398 chr12 113635055 chr20 40848410 chr15 59668078 chr12 10243158 chr18 46444366 chr12 58121508 chr15 59599521 chr15 56544942 chr18 20514217 chr12 64846499 chr16 75130142 chr12 20568666 chr18 12254784 chr14 105525484 chr5 168279190 chr12 83436758 chr13 92454487 chr3 48884826 chr15 67442588 chr3 195946597 chr20 7905990 chr20 24450876 chr19 13051211 chr17 19620263 chr15 84912101 chr11 35683582 chr12 117822199 chr3 149299399 chr22 35724388 chr22 39716213 chr12 13354616 chr22 36769509 chr12 49938027 chr22 38303393 chr16 85650395 chr5 149669433 chr14 72649687 chr6 167786484 chr14 105154994 chr13 28497621 chr16 28884493 chr12 65672082 chr2 217557616 chr13 24839413 chr3 21787630 chr17 47021520 chr22 36751194 chr6 108478563 chr15 79070483 chr13 111807510 chr6 111136859 chr15 43906817 chr13 103250163 chr14 104497547 chr5 128430539 chr3 4874239 chr6 78172784 chr14 23057952 chr3 179041743 chr13 39262227 chr13 36668831 chr12 27821943 chr15 72957488 chr2 20250672 chr12 48197110 chr14 96002525 chr16 87889666 chr12 62585750 chr11 130320107 chr2 69239871 chr6 7725842 chr15 75978879 chr6 154640863 chr18 59948461 chr15 81426597 chr13 73355806 chr12 6981014 chr20 48553244 chr14 69137081 chr10 70939275 chr20 61447334 chr12 54415147 chr18 29340825 chr12 124854907 chr13 94965396 chr3 184304408 chr15 67417860 chr2 29850455 chr6 169041074 chr16 87893023 chr14 70081079 chr12 72149118 chr15 71040854 chr17 77908058 chr12 111625057 chr17 15168099 chr3 138666240 chr18 61160438 chr14 105260982 chr5 177181499 chr3 138403527 chr11 69458502 chr20 524075 chr3 6946725 chr18 12883118 chr18 49866895 chr14 93074566 chr5 153418042 chr15 69452943 chr13 48612261 chr6 26597382 chr22 38202875 chr6 127836074 chr15 101866025 chr18 10740861 chr3 183945284 chr2 236401911 chr11 70397632 chr11 64643975 chr11 7563239 chr17 15902161 chr6 90061855 chr22 43670194 chr14 100020456 chr17 46125527 chr9 130829697 chr2 69171202 chr11 68848057 chr18 49902983 chr13 28366108 chr12 108079829 chr13 28496058 chr18 12912338 chr6 145865884 chr12 121124599 chr13 52202765 chr14 96893304 chr2 237479179 chr12 58003396 chr8 11415272 chr2 159651808 chr14 79032507 chr9 113785563 chr11 113953207 chr15 101866025 chr3 194407700 chr11 1474987 chr16 20444478 chr3 108203622 chr16 84902774 chr2 130738212 chr11 124767781 chr22 17971431 chr12 110563292 chr11 31841691 chr12 53400235 chr12 117756576 chr11 17553236 chr13 42032424 chr12 122235135 chr14 99984633 chr5 75698439 chr14 20925176 chr17 15139831 chr3 140795796 chr12 124965292 chr2 192015446 chr16 22220811 chr11 68181416 chr3 14692909 chr13 46356967 chr14 103576584 chr16 48468530 chr12 15941496 chr20 18269147 chr16 28374665 chr13 41364285 chr13 79194483 chr7 120969027 chr6 10842909 chr6 46597757 chr14 103864937 chr5 76932016 chr22 46344039 chr20 3761969 chr6 168843001 chr12 4810242 chr6 43244069 chr12 63543766 chr2 23747265 chr15 102042815 chr12 117674458 chr14 24566926 chr14 50154896 chr12 98911447 chr16 58069921 chr6 15597103 chr2 242147702 chr12 104156552 chr17 19028901 chr20 54580489 chr20 43513649 chr8 145010868 chr15 44486309 chr2 23718617 chr16 4942925 chr18 77166042 chr15 79576380 chr16 50583740 chr13 36050303 chr9 97889694 chr16 67841171 chr11 111957761 chr12 124811910 chr14 95658153 chr15 74364839 chr12 6331831 chr3 197687709 chr12 56115631 chr2 102423165 chr19 46992651 chr13 110951418 chr12 5678978 chr17 72958021 chr14 24641438 chr4 101719592 chr16 216561 chr17 76446984 chr11 1035109 chr6 160402911 chr13 110874842 chr14 78870082 chr3 101280900 chr11 63304614 chr17 76888499 chr3 42653997 chr14 105934555 chr12 122296446 chr6 149141140 chr11 67808203 chr12 124951222 chr3 145878214 chr20 52825772 chr6 116464670 chr3 31577139 chr15 69516868 chr14 101195354 chr17 2241533 chr12 95490776 chr20 61370545 chr14 34931900 chr11 3664603 chrX 49359038 chr14 104038779 chr6 35474148 chr13 39396050 chr3 156193747 chr14 68286442 chr22 25600824 chr3 183256169 chr3 145879316 chr15 67439562 chr20 31124002 chr16 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212603392 chr17 55953009 chr14 69861077 chr19 45575711 chr12 54653293 chr17 9331223 chr19 49642506 chr14 60462747 chr2 230499547 chr15 45421198 chr17 637070 chr8 10191232 chr16 29873147 chr12 2508695 chr14 24728926 chr16 5019032 chr14 88692995 chr18 74539147 chr15 31653107 chr14 61835153 chr13 80097622 chr11 126398134 chr18 11873008 chr12 119575245 chr11 68141850 chr15 53858451 chr14 78015650 chr12 49391731 chr12 39300318 chr17 74566299 chr16 2273434 chr5 176761538 chr13 99997673 chr22 38837189 chr16 87713080 chr4 6418422 chr22 38479288 chr14 99984701 chr22 23588333 chr6 84881773 chr17 76920337 chr14 30395697 chr15 90578500 chr2 96010988 chr14 72741187 chr15 42844381 chr12 57912738 chr14 76232925 chr16 2740054 chr11 124733477 chrX 23418321 chr15 39872902 chr7 102154954 chr15 31626478 chr3 184278810 chr15 99056821 chr12 109796911 chr20 61340657 chr16 83960069 chr12 103350479 chr11 21317728 chr12 57617584 chr12 3119176 chr17 38210783 chr13 26358849 chr15 31690233 chr3 124530718 chr2 60984163 chr19 2759241 chr20 18035242 chr14 51134117 chr11 370583 chr16 12020100 chr14 100020933 chr12 109796872 chr16 17454764 chr16 77884642 chr12 111604655 chr13 51098489 chr13 70358340 chr14 105945135 chr5 5179761 chr14 23901954 chr22 50764059 chr12 113902624 chr3 33259743 chr12 114371346 chr6 144675770 chr12 11948268 chr12 15366373 chr11 89537228 chr12 57524281 chr14 42169831 chr14 34640878 chr16 4974413 chr9 138597861 chr5 58633250 chr14 91827095 chr11 119236227 chr17 1686671 chr17 76888499 chr6 7729757 chr5 177811771 chr3 9005400 chr12 53773056 chr6 75956744 chr11 89602214 chr17 40832281 chr18 67070165 chr13 99918251 chr2 235873378 chr22 36783085 chr2 172388050 chr17 70810140 chr6 138825229 chr13 47216123 chr22 36960414 chrX 46616892 chr8 66955958 chr16 2204022 chr16 69354749 chr13 27998115 chr14 100069262 chr12 132322550 chr11 61215659 chr20 13878367 chr17 79970501 chr12 109252608 chr20 31677675 chr15 33625892 chr3 107318383 chr11 1987961 chr18 47786098 chr16 87890498 chr14 34393486 chr12 16086133 chr16 87661398 chr17 39769175 chr6 162040215 chr3 128839536 chrX 49178526 chr22 46344039 chr16 3148824 chr2 96051322 chr12 11954080 chr6 73330693 chr22 47338827 chr13 29233512 chr22 28246158 chr12 53298237 chr5 132158216 chr16 11768860 chr11 11613810 chr12 49934774 chrX 43832052 chr12 119584195 chr16 4049727 chr13 92084253 chr16 89387418 chr12 117827187 chr12 125028329 chr14 100007924 chr10 72576249 chr16 4268336 chr16 21448119 chr3 49044952 chr14 104614485 chr19 10810503 chr16 88837721 chr19 7032457 chr13 84455346 chr12 52628285 chr16 72047499 chr2 23907893 chr16 75105090 chr13 27999126 chr20 41200406 chr20 13254989 chr14 103864937 chr20 24608264 chr5 178287838 chr13 111831177 chr12 54425446 chr18 74188818 chr18 13912474 chr17 15552895 chr6 2902516 chr17 48912710 chr13 99687193 chr17 46621439 chr16 22330105 chr20 40100677 chr2 85638721 chr14 95693981 chr9 127703802 chr16 25711473 chr20 18693374 chr14 91471236 chr2 178078419 chr19 36631360 chr14 91855671 chr9 101570745 chr2 134023445 chr11 122848577 chr13 84454324 chr3 93605923 chr12 48187601 chr20 39976385 chr14 100204041 chr13 21407476 chr14 105881989 chr3 57260956 chr14 100573335 chrX 24071970 chr5 139488638 chr12 116641481 chr6 166749267 chr6 73356528 chr3 63474931 chr6 2891300 chr14 20295845 chr3 183945284 chr13 111085649 chr15 42360268 chr9 115513981 chr16 17322561 chr14 68282983 chr18 77199459 chr19 33792464 chr12 104070869 chr3 64547323 chr13 80914582 chr6 101846905 chr20 24639650 chr12 125004095 chr16 66505404 chr15 80861601 chr2 23611243 chr14 75128828 chr16 87725673 chr12 54338819 chr3 116382513 chr7 111845429 chr11 64646286 chr15 99271049 chr20 55975496 chr10 7861257 chr20 40172803 chr15 90718504 chr2 24582621 chr15 74724686 chr19 935267 chr7 65584898 chr15 54003232 chr13 110936343 chr12 96253464 chr17 78079671 chr20 24598154 chr12 584675 chr14 22958482 chr20 41620914 chr2 220094987 chr15 23811043 chr6 35778755 chr11 131407861 chr16 81898434 chr11 96059902 chrX 107018530 chr18 10740861 chr11 61197848 chr17 18941971 chr11 65292000 chr5 11632009 chr18 74125626 chr2 33668036 chr19 14184884 chr3 77331148 chr12 62586655 chr16 17199385 chr7 150707235 chr13 74425315 chr17 72341014 chr11 2859186 chr20 45618201 chr15 29504631 chr10 49732876 chr12 117771727 chr12 1704443 chr20 1103991 chr19 46195136 chr12 56116227 chr20 20374037 chr11 35641938 chr16 4815786 chr19 44764837 chr13 50932095 chr14 74607285 chr5 38583054 chr12 49719047 chr12 109716912 chr14 90863600 chr12 53784323 chr3 79815729 chr15 75109505 chr2 63278108 chr14 24778911 chr16 89574022 chr15 79096751 chr9 21973527 chr2 77820399 chr18 72917447 chr17 46221813 chr2 85553813 chr14 74033301 chr16 87893470 chr15 40456724 chr5 149867186 chr11 68699932 chr12 111332408 chr14 77491876 chr16 70722541 chr5 169063590 chr18 10463531 chr19 2867898 chr17 42966379 chr13 111365899 chr17 19551214 chr5 179344751 chr5 145583807 chr2 220110584 chr6 37244858 chr19 48673525 chr12 29430585 chr19 18706598 chr3 122514476 chr15 65188459 chr3 49029310 chr12 54427310 chr2 7118707 chr20 61444138 chr15 101877370 chr18 25730190 chr3 133659690 chr11 44601199 chr20 5765597 chr2 176945893 chr14 77669529 chr15 68051838 chr16 88812638 chr2 239009050 chr7 158888063 chr14 58640305 chr13 111108504 chr12 108079458 chr5 76935246 chr18 12912293 chr15 78930633 chr8 143918218 chr12 123753032 chr2 9562567 chr12 49257664 chr16 70285978 chr12 124847753 chr17 72340380 chr3 4822623 chr15 101442826 chr5 52918659 chr12 124897560 chr12 103285072 chr11 68139098 chr6 76060940 chr11 68149325 chr17 77909749 chr11 69089564 chr15 75190716 chr11 89606016 chr14 105529553 chr3 143690246 chr15 74365266 chr20 55981467 chr20 23028785 chr2 172172747 chr19 19248569 chr6 90170712 chr6 170892994 chr22 47549830 chr14 74807607 chr2 46844498 chr11 61451702 chr6 76059734 chr22 38477780 chr9 24542255 chr6 131285322 chr12 105031680 chr18 56531628 chr12 2278951 chr16 55478577 chr5 78279882 chr15 73631717 chr11 2710838 chr12 15275410 chr19 4455413 chr12 54350294 chr12 85631372 chr16 87698990 chr6 142622584 chr6 37894682 chr15 85359523 chr7 155599942 chr17 73030211 chr15 67417860 chr17 48261653 chr14 54863719 chr12 69005196 chr14 34864772 chr22 28277628 chr3 31900140 chr11 70956646 chr17 9804778 chr13 110927758 chr8 87881603 chr3 184301518 chr6 39787507 chr3 50365476 chr14 72857101 chr11 44628644 chr2 10538297 chr14 52478367 chr11 21386631 chr15 75336956 chr20 30034416 chr11 68138850 chr11 61486497 chr18 77218474 chr15 72511414 chr5 905692 chr5 138284831 chr3 196467917 chr6 74223642 chr2 152894427 chr20 10614679 chr20 37274925 chr22 37914655 chr13 111298808 chr7 122064307 chr12 52301505 chr12 95551716 chr11 95976442 chr14 20925263 chr12 2268381 chr9 21996690 chr9 132460314 chr17 6312011 chr22 41866490 chr15 67460700 chr12 14060146 chr5 177034561 chr2 25139131 chr19 18836407 chr11 72525927 chr20 37257596 chr12 117884597 chr14 99981191 chr12 56211874 chr14 69070944 chr22 46326806 chr15 79007816 chr17 80225605 chr16 88844415 chr20 388144 chr20 25746002 chr9 139686019 chr19 405313 chr17 77764398 chr14 92981723 chr11 123045794 chr5 171646468 chr12 94543524 chr6 148664420 chr13 113758242 chr11 189833 chr9 21995197 chr11 114050079 chr15 41244632 chr13 42032635 chr15 40545511 chr19 30889459 chr6 78172277 chr3 128744760 chr3 98560883 chr15 78942436 chr5 40680446 chr22 28186862 chr9 135546700 chr2 227661381 chr5 7820781 chr20 13204581 chr20 6101929 chr19 11529574 chr9 139939347 chr18 18606618 chr17 72767008 chr16 87889666 chr3 79815007 chr2 96801090 chr12 122232323 chr17 21477645 chr13 39262227 chr18 77245487 chr20 57471122 chr11 31846188 chr5 99878914 chr18 21769429 chr14 90868250 chr15 92407548 chrX 48547839 chr9 126792233 chr14 61110002 chr11 61468526 chr12 6450539 chr12 25102196 chr12 101787956 chr3 58038562 chr19 50193737 chr11 61342332 chr17 42336687 chr6 40381264 chr18 57101415 chr18 25755897 chr11 62455849 chr13 36101743 chr6 136335824 chr11 72396829 chr9 34724831 chr20 35673037 chr22 31556828 chr13 111869203 chr8 10131565 chr11 6440614 chr14 102742517 chr19 13512786 chr11 71949351 chr5 172272430 chr17 46226125 chr13 96131459 chr14 69070659 chr12 51736360 chr11 126188475 chr20 1163295 chr16 66550612 chr6 17485659 chr3 60316163 chr20 36662866 chr19 11435430 chr22 29650483 chr19 58095699 chr12 104156552 chr14 103513151 chr19 7032549 chr6 19839518 chr19 48821028 chr12 65672082 chr5 75867305 chr12 83248478 chr12 11872884 chr14 77600217 chr15 51998416 chr20 13255338 chr12 58088019 chr17 77991007 chr5 6453988 chr16 89470029 chr17 54398065 chr22 41214867 chr16 31885529 chr17 74897884 chr19 1967352 chr11 118793284 chr13 99635091 chr19 8190876 chr17 40260704 chr12 125017105 chr12 117805057 chr12 54388821 chr18 47482543 chr19 19367084 chr2 42795242 chr18 21512521 chr11 27016530 chr16 17563004 chr4 789158 chr4 174444205 chr5 121297915 chr20 31136845 chr10 23633690 chr12 117317704 chr17 40018828 chr7 99614007 chr22 20302404 chr9 6414308 chr22 37536084 chr11 65314498 chr11 61341207 chr12 62606860 chr6 166744279 chr20 36707837 chr10 4973799 chr13 108303589 chr19 46269978 chr3 21822610 chr6 43483025 chr12 124826078 chr16 17469594 chr22 43593595 chr12 56137637 chr14 68286569 chr13 76174688 chr3 196738111 chr6 157978863 chr20 8628780 chr17 28804401 chr6 96480082 chr18 57220985 chr2 212319644 chr14 65512753 chr3 15470158 chr17 73876534 chr22 29652183 chr20 47589574 chr11 69175088 chr12 125023676 chr17 29284048 chr18 72175316 chr20 31129482 chr12 53343479 chr12 11874044 chr18 61088618 chr18 70213394 chr12 14114379 chr17 7153738 chr20 3139415 chr5 180059067 chr20 60791865 chr3 178867159 chr12 48171878 chr12 4396004 chr5 7851285 chr11 120096499 chr11 2800586 chr20 633507 chr20 54580489 chr20 2539227 chr14 70085866 chr14 102719349 chr3 126259929 chr20 49163358 chr15 52632412 chr11 70478821 chr20 55754230 chr16 11768860 chr2 54954699 chr3 196595774 chr13 107143980 chr18 7047336 chr14 104001122 chr20 32255692 chr11 111285431 chr11 65559288 chr14 69162068 chr6 13356417 chr22 37536737 chr19 5059507 chr13 27999126 chr5 149430689 chr16 2198097 chr11 64761978 chr2 235936653 chr6 1393482 chr19 37555642 chr15 43976544 chr14 74485639 chr3 9872147 chr18 44552959 chr13 70358340 chr6 24910750 chr6 127836074 chr3 175338932 chr6 27834959 chr6 41156642 chr3 117631830 chr22 38382245 chr18 77905127 chr19 1210522 chr2 119603285 chr11 35302805 chr3 185225016 chr19 46032329 chr16 58718950 chr5 59190048 chr10 26504425 chr14 105715553 chr12 54666945 chr17 32911834 chr2 3828507 chr20 48733402 chr6 43213374 chr11 114050079 chr22 32955536 chr15 65219093 chr14 76178021 chr14 61430527 chr14 38073396 chr17 73839630 chr5 38846973 chr13 47128881 chr2 33701712 chr20 62173763 chr12 49939540 chr11 73693059 chr13 93962880

The predictive power of each CpG site may be ranked by the P-value of the individual sites in differentiating between non-CP and CP patients. Table 7 ranks the top 1000 sites by P-value.

TABLE 7 Blood Muscle Satellite CpG Site CpG Site CpG Site chr3.0170984628 chr16.0002184051 chr22.0041683914 chr12.0113912958 chr17.0032964775 chr3.0051997994 chr5.0021333675 chr20.0060998493 chr11.0093971657 chr1.0000565262 chr17.0034497913 chr20.0022553062 chr18.0059002180 chr13.0050656192 chr20.0060375363 chr22.0021469408 chr9.0090747955 chr12.0001742005 chr16.0002689275 chr17.0056596237 chr19.0048673525 chr12.0006446797 chr15.0031516141 chr16.0058069921 chr15.0028343785 chr17.0018941025 chr18.0071801714 chr6.0161033995 chr6.0161034892 chr15.0092982723 chr18.0004068725 chr11.0066189251 chr16.0002176197 chr12.0001704443 chr12.0057869596 chr11.0017593831 chr11.0013984067 chr16.0014782082 chr4.0101719592 chr2.0243078103 chr18.0024130101 chr14.0101270192 chr19.0020188618 chr16.0067564144 chr13.0113650227 chr6.0169653176 chr14.0019641888 chr19.0019007351 chr6.0007394523 chr6.0139013304 chr18.0043923940 chr6.0117587149 chr14.0095048461 chr12.0119584195 chr12.0058160354 chr16.0002184447 chr2.0056193463 chr13.0033220266 chr14.0038061691 chr12.0002513357 chr12.0002113367 chr6.0041528356 chr13.0028891055 chr13.0114547107 chr17.0065040349 chr22.0046279322 chr18.0029214163 chr6.0043445772 chr11.0123045794 chr11.0071160096 chr17.0019045779 chr5.0145724640 chr3.0182928999 chr6.0161062626 chr9.0043084487 chr6.0150284688 chr6.0100901811 chr15.0067989241 chr11.0093475384 chr13.0028196417 chr15.0069824154 chr16.0030886974 chr16.0019728830 chr12.0116068191 chr17.0007975795 chr14.0076447816 chr12.0133301799 chr6.0167001337 chr16.0021504797 chr18.0011747918 chr22.0038022735 chr12.0130645000 chr16.0073089847 chr12.0108079458 chr20.0061696282 chr16.0000680326 chr11.0000188098 chr9.0097811271 chr17.0075149309 chr3.0147130343 chr6.0099969527 chr14.0034393486 chr13.0050656618 chr12.0058088346 chr11.0067044849 chr3.0197687858 chr3.0059803935 chr12.0001609391 chr6.0149354426 chr12.0040909296 chr15.0090964193 chr6.0026235050 chr6.0050811344 chr20.0048793087 chr17.0011145564 chr15.0082977792 chr17.0078426681 chr9.0033025770 chr11.0070664922 chr12.0011513104 chr12.0123009847 chr12.0108040090 chr5.0172124187 chr15.0075932985 chr11.0069257964 chr20.0019221684 chr11.0094276724 chr14.0081040927 chr20.0019447811 chr18.0003771925 chr9.0045729679 chr20.0035217888 chr7.0130353922 chr2.0011879322 chr2.0029850455 chr3.0019188810 chr3.0119422009 chr18.0077209053 chr18.0019674041 chr17.0026166996 chr20.0060893697 chr12.0121082579 chr14.0057284380 chr13.0113705362 chr13.0103425377 chr12.0089410897 chr2.0239051141 chr12.0069005196 chr11.0000796607 chr14.0105643016 chr6.0042418413 chr5.0126641436 chr22.0040899482 chr17.0027482390 chr18.0019064708 chr14.0065204158 chr2.0133110495 chr12.0006437021 chr13.0093896533 chr12.0004758511 chr16.0066864962 chr3.0122711856 chr22.0033197965 chr5.0034839641 chr18.0044547036 chr19.0000920756 chr11.0125774368 chr16.0066879958 chr17.0036286187 chr3.0029361462 chr12.0016644803 chr5.0140782367 chr18.0074700260 chr11.0129750009 chr6.0021594873 chr12.0049484577 chr19.0011533307 chr20.0058801846 chr20.0061703026 chr3.0130802181 chr13.0093896533 chr6.0064283735 chr18.0045011716 chr16.0014818378 chr16.0005573968 chr12.0131689822 chr16.0058000211 chr14.0019400285 chr16.0002004921 chr19.0040723542 chr20.0034287732 chr3.0117631830 chr2.0056193463 chr8.0086756044 chr22.0038022735 chr12.0132855014 chr6.0143859047 chr22.0020779274 chr16.0050582980 chr19.0015580788 chr12.0129065948 chr12.0006663682 chr22.0024816977 chr3.0016939628 chr20.0020258001 chr14.0019902538 chr12.0010243158 chr15.0099344316 chr11.0122933736 chr12.0057608666 chr17.0004850081 chr14.0067984108 chr15.0101588506 chr20.0043513649 chr13.0109856377 chr12.0083436417 chr13.0028497262 chr17.0011145564 chr18.0006284010 chr20.0021689463 chr20.0031330621 chr14.0093019588 chr20.0048919181 chr5.0065124116 chr2.0071533997 chr22.0037977772 chr3.0128719633 chr16.0084054247 chr3.0147128690 chr18.0044556541 chr4.0095555981 chr15.0060302054 chr3.0132136984 chr3.0138666240 chr15.0084114534 chr6.0030640440 chr2.0035092870 chr10.0104179528 chr12.0003207132 chr20.0025001878 chr16.0070557879 chr16.0015239520 chr6.0016145414 chr3.0004508116 chr18.0077559128 chr16.0003238806 chr11.0006633681 chr15.0102331212 chr12.0101447687 chr20.0009100637 chr12.0119596461 chr5.0177181499 chr19.0001238477 chr14.0052266868 chr14.0069861077 chr10.0081665235 chr14.0088459020 chr12.0106978718 chr13.0021069344 chr19.0048836554 chr12.0103344694 chr12.0005019351 chr2.0011878864 chr9.0008638390 chr6.0161067521 chr2.0220379058 chr6.0159600100 chr6.0134210544 chr5.0034182070 chr19.0007038916 chr18.0071642546 chr11.0043605047 chr17.0073069667 chr18.0012287195 chr14.0100626499 chr17.0036292033 chr12.0071439895 chr5.0168726909 chr5.0177219938 chr14.0101308437 chr3.0048884826 chr14.0053155967 chr3.0013541769 chr11.0075162684 chr15.0069452943 chr3.0188420144 chr14.0020089147 chr2.0023747265 chr15.0075072612 chr6.0028831484 chr17.0018941025 chr6.0036737891 chr8.0106331523 chr5.0164550214 chr14.0080170888 chr6.0027776053 chr17.0038475164 chr14.0103575195 chr19.0047733365 chr5.0122422526 chr17.0001390159 chr16.0084212059 chr3.0170886184 chr6.0033280212 chr2.0136874432 chr14.0104190006 chr14.0052119953 chr12.0045006632 chr12.0130645000 chr3.0032022182 chr12.0054376047 chr20.0059927068 chr8.0025900066 chr20.0019419638 chr6.0164766175 chr18.0057357804 chr16.0053738156 chr14.0101909600 chr20.0048552544 chr6.0073879011 chr14.0106437080 chr12.0003241735 chr14.0103984664 chr17.0079292270 chr13.0096206439 chr16.0050746190 chr14.0104465222 chr17.0046675549 chr16.0088271806 chr19.0016830739 chr17.0078944136 chr3.0141746797 chr11.0002405177 chr16.0032773264 chr15.0059668078 chr15.0069516868 chr6.0145853785 chr10.0023479600 chr17.0074566299 chr13.0068862091 chr5.0129242435 chr9.0133777218 chr18.0010938440 chr20.0052660313 chr2.0218771815 chr13.0041796041 chr16.0072883281 chr12.0006104973 chr2.0200819443 chr15.0027604283 chr3.0189596966 chr11.0032113404 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EQUIVALENTS

Although preferred embodiments of the invention have been described using specific terms, such description is for illustrative purposes only, and it is to be understood that changes and variations may be made without departing from the spirit or scope of the following claims.

INCORPORATION BY REFERENCE

The entire contents of all patents, published patent applications, and other references cited herein are hereby expressly incorporated herein in their entireties by reference. 

1. A method of detecting cerebral palsy in a subject, the method comprising: determining a methylation state for each of a plurality of cytosine-guanine dinucleotide (CpG) sites in a sample obtained from the subject, calculating a differential methylation level based on the methylation states of the plurality of CpG sites, and comparing the differential methylation level to a predetermined reference level, wherein when the differential methylation level deviates from the predetermined reference level, the presence of cerebral palsy is indicated in the patient.
 2. The method of claim 1 wherein the plurality of CpG sites comprises at least one selected from the CpG sites listed in Table 4, Table 5, Table 6 or Table
 7. 3. The method of claim 1 wherein the plurality of CpG sites comprises at least five selected from the CpG sites listed in Table 4, Table 5, Table 6 or Table
 7. 4. The method of claim 1 wherein the plurality of CpG sites comprises at least ten selected from the CpG sites listed in Table 4, Table 5, Table 6 or Table
 7. 5. The method of claim 1 wherein the plurality of CpG sites comprises at least m % selected from the top n most predictive CpG sites listed in Table 4 or Table 5, wherein: m is selected from the group consisting of: 50, 60, 70, 80, 90, 95, and 99; and n is selected from the group consisting of 100, 500, 1,000, 2,000, and 2,500.
 6. The method of claim 1, further comprising: providing treatment for cerebral palsy to the patient when cerebral palsy is indicated.
 7. The method of claim 6 wherein treatment for cerebral palsy comprises the administration of medication, therapy or surgery.
 8. The method of claim 1 wherein the plurality of CpG sites comprises: a plurality of up sites, and a plurality of down sites, wherein: methylation at the up sites indicates that the likelihood the patient has cerebral palsy is increased, and methylation at the down sites indicates that the likelihood the patient has cerebral palsy is decreased, and wherein calculating a differential methylation level comprises adding in a linear weighted summation values based on the methylation states of the up sites from a value based on the methylation states of the down sites.
 9. The method of claim 1, wherein the sample is selected from the group consisting of a peripheral blood mononuclear cell sample, a blood sample, a muscle sample or a satellite cell sample. 